Merge pull request #822 from KevinMenden/yaml-load-exception

linting: better error message to yaml loading

nf_core/lint/actions_awsfulltest.py

@@ -35,8 +35,8 @@ def actions_awsfulltest(self):
         try:
             with open(fn, "r") as fh:
                 wf = yaml.safe_load(fh)
-        except:
-            return {"failed": ["Could not parse yaml file: {}".format(fn)]}
+        except Exception as e:
+            return {"failed": ["Could not parse yaml file: {}, {}".format(fn, e)]}
 
         aws_profile = "-profile test "
 

nf_core/lint/actions_awstest.py

@@ -30,8 +30,8 @@ def actions_awstest(self):
     try:
         with open(fn, "r") as fh:
             wf = yaml.safe_load(fh)
-    except:
-        return {"failed": ["Could not parse yaml file: {}".format(fn)]}
+    except Exception as e:
+        return {"failed": ["Could not parse yaml file: {}, {}".format(fn, e)]}
 
     # Check that the action is only turned on for workflow_dispatch
     try:

nf_core/lint/actions_branch_protection.py

@@ -76,8 +76,8 @@ def actions_branch_protection(self):
     try:
         with open(fn, "r") as fh:
             branchwf = yaml.safe_load(fh)
-    except:
-        return {"failed": ["Could not parse yaml file: {}".format(fn)]}
+    except Exception as e:
+        return {"failed": ["Could not parse yaml file: {}, {}".format(fn, e)]}
 
     # Check that the action is turned on for PRs to master
     try:

nf_core/lint/actions_ci.py

@@ -80,8 +80,8 @@ def actions_ci(self):
     try:
         with open(fn, "r") as fh:
             ciwf = yaml.safe_load(fh)
-    except:
-        return {"failed": ["Could not parse yaml file: {}".format(fn)]}
+    except Exception as e:
+        return {"failed": ["Could not parse yaml file: {}, {}".format(fn, e)]}
 
     # Check that the action is turned on for the correct events
     try:

nf_core/lint/actions_lint.py

@@ -63,8 +63,8 @@ def actions_lint(self):
         try:
             with open(fn, "r") as fh:
                 lintwf = yaml.safe_load(fh)
-        except:
-            return {"failed": ["Could not parse yaml file: {}".format(fn)]}
+        except Exception as e:
+            return {"failed": ["Could not parse yaml file: {}, {}".format(fn, e)]}
 
         # Check that the action is turned on for push and pull requests
         try: